walterst

#!/usr/bin/env python
from __future__ import division
# USAGE: python parse_ipod_to_metadata.py mapping_file days_to_consider ipod_tab_delim_file raw_output_file qiime_compatible_output_file
# where days_to_consider counts the same-day as one of the days, and comma-seperated columns needs to be
# an exact match to the field label in the ipod data file, e.g. Gastrointestinal_issues
# All dates must be in the format of DD/MM/YY in the ipod source tab delimited data.


from sys import argv
from operator import itemgetter

walterst

#!/usr/bin/env

from sys import argv
from random import random

#from gzip import open as gz_open
from glob import glob

import gzip
import os

walterst

#!/usr/bin/env python

# Used to find fastq seqs in gzipped files, write first error, if any, to a log file
# Usage:  python find_fastq_errors.py fastq_folder log_file
# where fastq_folder has all of the fastq files in it-will search subdirectories

from sys import argv
from glob import glob

import gzip

walterst

#!/usr/bin/env python

"""Usage: python record_singletons.py X Y
where X is the input OTU mapping file and Y is the output singleton sequence ID file.
"""

from sys import argv

otu_mapping = open(argv[1], "U")
singletons_out = open(argv[2], "w")

walterst

#!/usr/bin/env python

""" This is modified from the bfillings usearch app controller

usage: python parse_otu_mapping_from_uc.py X Y
where X is the input .uc file, Y is the output OTU mapping file"""


from sys import argv

walterst

#!/usr/bin/env python

from sys import argv

from operator import itemgetter
from scipy.stats import rankdata
from numpy import log

from biom import load_table

walterst

#!/usr/bin/env python


# Usage:  python filter_barcode_header.py original_barcode_seqs.fastq new_barcode_seqs.fastq
# WARNING-the second file specified will be overwritten if it exists!

bc_start_indicator = "1:N:0:"
chars_to_strip = ["+"]

from sys import argv

walterst

#!/usr/bin/env python

# Used to count fastq seqs in gzipped files, write counts and file name to log file
# Usage:  python count_zipped_fastq_reads.py fastq_folder log_file
# where fastq_folder has all of the fastq files in it (doesn't search subdirectories)

from sys import argv
from glob import glob

from cogent.parse.fastq import MinimalFastqParser

walterst

#!/usr/bin/env python

# Used to filter a fastq to match another fastq that is a subset of the query one, e.g. matching a
# index fastq to the pear assembled subset fastq
# Usage:  python filter_fastq.py input_fastq target_fastq output_fastq

from sys import argv

from cogent.parse.fastq import MinimalFastqParser
from qiime.util import gzip_open

walterst

#!/usr/bin/env python

# Used to filter a fastq to match another fastq that is a subset of the query one, e.g. matching a
# index fastq to the pear assembled subset fastq
# Usage:  python filter_fastq.py input_fastq target_fastq output_fastq

from sys import argv

from cogent.parse.fastq import MinimalFastqParser